[gmx-users] how to generate .top file

[Lovika Moudgil]

Thanks Tsjerk .... [?]


Regards
Lovika


On Fri, May 23, 2014 at 4:17 PM, Tsjerk Wassenaar <tsjerkw at gmail.com> wrote:

> Hi Lovika,
>
> Yes, you can
>
> #include "gold.itp"
>
> or something along those lines.
>
> Cheers,
>
> Tsjerk
>
>
> On Fri, May 23, 2014 at 12:44 PM, Lovika Moudgil <lovikamoudgil at gmail.com
> >wrote:
>
> > Thanks for reply Abhijit... .I will definitely try this .
> >
> > Hey Tsjerk ... Is it possible , if I define all this in a different  .itp
> > and than define that .itp file in .top file ?????
> >
> >
> > On Fri, May 23, 2014 at 3:45 PM, Tsjerk Wassenaar <tsjerkw at gmail.com>
> > wrote:
> >
> > > Hi Lovika,
> > >
> > > IIRC your gold is frozen, right? So you have a moleculetype definition
> > for
> > > one gold atom (atomtype, mass, charge). You can just put it in the .top
> > > file after the #includes of the force field, like
> > >
> > > #include "forcefield.itp"
> > > #include "protein.itp"
> > >
> > > [ moleculetype ]
> > > AU          1
> > >
> > > [ atoms ]
> > > 1       AU      1       UA          UA       1      0        196.96655
> > >
> > > [ system ]
> > > Protein with gold
> > >
> > > [ molecules ]
> > > ...
> > >
> > >
> > > Hmm, I wonder, should one account for the gravitational effects of
> gold.
> > > Pretty heavy stuff :p
> > >
> > > Cheers,
> > >
> > > Tsjerk
> > >
> > >
> > >
> > > On Fri, May 23, 2014 at 11:39 AM, Lovika Moudgil <
> > lovikamoudgil at gmail.com
> > > >wrote:
> > >
> > > > Hi everyone..
> > > > I have a .pdb file with protein and gold slab .Problem is I can
> > generate
> > > > .top file for  my protein with pdb2gmx but I want my slab in the same
> > > > system .I can generate .gro file for both but what about .top file .
> > Can
> > > > any body help me with this issue .Thanks in advance.
> > > >
> > > > Regards
> > > > Lovika
> > > > --
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> > >
> > > --
> > > Tsjerk A. Wassenaar, Ph.D.
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>
> --
> Tsjerk A. Wassenaar, Ph.D.
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